Merge branch 'develop' into feature/functional_plugin_api

4DNucleome · Jan 26, 2024 · a104055 · a104055
2 parents ad9946a + de43a4f
commit a104055
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diff --git a/.github/workflows/base_test_workflow.yml b/.github/workflows/base_test_workflow.yml
@@ -1,3 +1,5 @@
+name: Base Test Workflow
+
 on:
   workflow_call:
     inputs:
@@ -40,7 +42,7 @@ jobs:
     runs-on: ${{ inputs.os }}
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python ${{ inputs.python_version }}
         with:
           python-version: ${{ inputs.python_version }}
@@ -69,7 +71,7 @@ jobs:
 
       - name: Download test data
         if: ${{ inputs.test_data }}
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -80,7 +82,7 @@ jobs:
           pip list
 
       - name: Test with tox
-        uses: aganders3/headless-gui@v1
+        uses: aganders3/headless-gui@v2
         timeout-minutes: ${{ inputs.timeout }}
         with:
           run: python -m tox ${{ inputs.tox_args }}
@@ -90,31 +92,17 @@ jobs:
           BACKEND: ${{ inputs.qt_backend }}
           PIP_CONSTRAINT: requirements/constraints_py${{ inputs.python_version }}.txt
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: upload pytest timing reports as json
+          name: timing-report-${{ inputs.os }}-py-${{ inputs.python_version }}-${{ inputs.napari }}-${{ inputs.qt_backend }}-${{ inputs.coverage }}
           path: |
             ./report-*.json
           retention-days: 7
 
-      - uses: actions/upload-artifact@v3
+      - name: Upload coverage data
+        uses: actions/upload-artifact@v4
         if: ${{ inputs.coverage }}
         with:
-          name: coverage_report ${{ inputs.tox_args }}
+          name: cov-reports-${{ inputs.os }}-py-${{ inputs.python_version }}-${{ inputs.napari }}-${{ inputs.qt_backend }}
           path: |
-            ./htmlcov
-          retention-days: 7
-
-      - uses: codecov/codecov-action@v3
-        if: ${{ inputs.coverage }}
-        with:
-          file: ./coverage.xml
-          fail_ci_if_error: true
-          token: ${{ secrets.CODECOV_TOKEN }}
-
-      - name: Upload coverage
-        uses: actions/upload-artifact@v3
-        with:
-          name: coverage
-          path: ./coverage.xml
-          retention-days: 5
+            ./.coverage.*
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -47,7 +47,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -58,7 +58,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -72,4 +72,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
diff --git a/.github/workflows/semgrep.yml b/.github/workflows/semgrep.yml
@@ -28,7 +28,7 @@ jobs:
 
     steps:
       # Fetch project source with GitHub Actions Checkout.
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       # Run the "semgrep ci" command on the command line of the docker image.
       - run: semgrep ci
         env:

diff --git a/.github/workflows/test_napari_repo.yml b/.github/workflows/test_napari_repo.yml
@@ -15,7 +15,7 @@ jobs:
       - shell: bash
         run: bash build_utils/download_data.sh
       - name: Upload test data
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -35,7 +35,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
 
@@ -54,14 +54,14 @@ jobs:
           pip install setuptools tox tox-gh-actions
 
       - name: Download test data
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: test_data
           path: test_data
 
       - name: Test with tox
         # run tests using pip install --pre
-        uses: aganders3/headless-gui@v1
+        uses: aganders3/headless-gui@v2
         timeout-minutes: 60
         with:
           run: tox

diff --git a/.github/workflows/test_prereleases.yml b/.github/workflows/test_prereleases.yml
@@ -23,7 +23,7 @@ jobs:
       - shell: bash
         run: bash build_utils/download_data.sh
       - name: Upload test data
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -43,7 +43,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           cache: 'pip'
@@ -59,7 +59,7 @@ jobs:
       - uses: tlambert03/setup-qt-libs@v1
 
       - name: Download test data
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -71,7 +71,7 @@ jobs:
 
       - name: Test with tox linux
         # run tests using pip install --pre
-        uses: aganders3/headless-gui@v1
+        uses: aganders3/headless-gui@v2
         timeout-minutes: 60
         with:
           run: python -m tox -v --pre
@@ -100,7 +100,7 @@ jobs:
     runs-on: "ubuntu-latest"
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       name: Install Python 3.9
       with:
         python-version: 3.9
@@ -115,19 +115,19 @@ jobs:
         pip-sync
         pip install .
     - name: upload requirements
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: requirements
         path: requirements.txt
     - name: Run PyInstaller
       run: python  build_utils/create_and_pack_executable.py
     - name: Upload bundle
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: bundle
         path: dist2/
     - name: Test bundle
-      uses: aganders3/headless-gui@v1
+      uses: aganders3/headless-gui@v2
       timeout-minutes: 60
       with:
         run: dist/PartSeg/PartSeg _test

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -25,7 +25,7 @@ jobs:
       - shell: bash
         run: bash build_utils/download_data.sh
       - name: Upload test data
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -102,8 +102,8 @@ jobs:
     uses: ./.github/workflows/base_test_workflow.yml
     with:
       test_data: True
-      python_version: "3.8"
-      tox_args: "-e py38-PyQt5-coverage"
+      python_version: "3.10"
+      tox_args: "-e py310-PyQt5-coverage"
       coverage: true
 
   test_minimal:
@@ -116,6 +116,48 @@ jobs:
       tox_args: "-e py38-PyQt5-minimal"
       coverage: true
 
+  coverage_prepare:
+    name: Prepare coverage
+    runs-on: ubuntu-latest
+    needs: [test_coverage, test_minimal]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+          cache-dependency-path: setup.cfg
+          cache: 'pip'
+      - name: Install Dependencies
+        run: |
+          pip install --upgrade pip
+          pip install codecov
+
+      - name: Download coverage data
+        uses: actions/download-artifact@v4
+        with:
+          pattern: cov-reports-*
+          path: coverage
+          merge-multiple: true
+      - name: combine coverage data
+        run: |
+          python -Im coverage combine coverage
+          python -Im coverage xml -o coverage.xml
+          # Report and write to summary.
+          python -Im coverage report --format=markdown --skip-empty --skip-covered >> $GITHUB_STEP_SUMMARY
+
+      - name: Upload coverage artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage_xml
+          path: coverage.xml
+          retention-days: 5
+
+      - name: Upload coverage data
+        uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
   test_conda:
     name: Test PartSeg conda
     runs-on: ubuntu-20.04
@@ -135,7 +177,7 @@ jobs:
       - uses: tlambert03/setup-qt-libs@v1
 
       - name: Download test data
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -160,7 +202,7 @@ jobs:
         run: bash build_utils/create_environment_yml.sh
 
       - name: Upload environment file
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: environment
           path: environment.yml
@@ -171,7 +213,7 @@ jobs:
         run: sed -e "s/{sys_platform}/{platform}/g" tox.ini -i
 
       - name: Test with tox
-        uses: aganders3/headless-gui@v1
+        uses: aganders3/headless-gui@v2
         with:
           run: conda run -n test --no-capture-output tox -e py39-PySide2-conda
         timeout-minutes: 60
@@ -184,4 +226,4 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: hynek/build-and-inspect-python-package@v1
+      - uses: hynek/build-and-inspect-python-package@v2
diff --git a/.github/workflows/upgrade-dependencies.yml b/.github/workflows/upgrade-dependencies.yml
@@ -22,22 +22,22 @@ jobs:
           ssh-key: ${{ secrets.DEPLOY_KEY }}
 
       # START PYTHON DEPENDENCIES
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.8"
           cache: pip
           cache-dependency-path: 'setup.cfg'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.9"
           cache: pip
           cache-dependency-path: 'setup.cfg'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
           cache: pip
           cache-dependency-path: 'setup.cfg'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           cache: pip
@@ -53,6 +53,7 @@ jobs:
             python${pyv}  -m pip install -U pip pip-tools
             python${pyv}  -m piptools compile --upgrade -o requirements/constraints_py${pyv}.txt  setup.cfg requirements/version_denylist.txt ${flags}
           done
+          python3.11 -m piptools compile --upgrade -o requirements/constraints_py3.11_docs.txt  setup.cfg requirements/version_denylist.txt --allow-unsafe --strip-extras --extra docs --extra pyqt6
       # END PYTHON DEPENDENCIES
 
       - name: Check updated packages

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.10.1
+    rev: 23.12.1
     hooks:
     - id: black
       pass_filenames: true
@@ -25,7 +25,7 @@ repos:
     - id: setup-cfg-fmt
       args: ["--include-version-classifiers", "--max-py-version", "3.11"]
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.1.14
     hooks:
       - id: ruff
 -   repo: https://github.com/asottile/pyupgrade
@@ -49,7 +49,7 @@ repos:
           - mdformat-toc
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.6.1'  # Use the sha / tag you want to point at
+    rev: 'v1.8.0'  # Use the sha / tag you want to point at
     hooks:
     -   id: mypy
         files: ^package/PartSegImage/.+\.py

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -17,15 +17,16 @@ sphinx:
 formats: all
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - requirements: requirements/constraints_py3.9.txt
-    - requirements: requirements/requirements_dev.txt
+    - requirements: requirements/constraints_py3.11_docs.txt
     - method: pip
-      path: .[docs]
+      path: .
+      extra_requirements:
+        - docs